Influenza A virus is a major human respiratory pathogen, and available vaccines and antivirals are of limited efficacy, especially in the elderly and during pandemic years. Influenza virus pathogenesis has two driving forces, virus replication and host responses. In order to identify novel targets for therapeutic intervention during influenza virus infection, we have assembled an interdisciplinary team that uses a highly integrated systems biology approach to identify and validate key early genes/networks involved in virus pathogenesis. Our overall underlying hypothesis is that host genes and networks involved in viral replication and in host response represent targets for therapeutic intervention. In order to identify these networks we propose to integrate into predictive and comprehensive models OMICS responses during influenza virus infection in ex vivo relevant human cells (Project 1) and in an animal model of influenza virus infection (Project 2). Our proposed research will compare systematically three clinically relevant influenza virus strains that differ in virulence both in mice and in humans. Core E will construct models by the integration of functional genomics, epigenomics, transcriptomics (Core B), proteomics (including post-translational modifications, Core C) and metabolomics (Core D) that will result in the identification of key genes, networks and subnetworks likely to be involved in virus replication and host responses. We propose an innovate modeling approach (Core E) based on acquisition of global OMICS data followed by model refinement using focused targeted-OMICS approaches, which allows for an extensive experimental interrogation of the generated models. The identified network nodes and subnetworks by these models will be validated and interrogated using targeted -OMICS in Projects 1 and 2 by conducting perturbations including: use of specific virus mutants that disrupt key host-virus interactions, use of host gene inhibitors, and use of mouse k.o. and antisense targeting of key host genes in a mouse model. The results of these perturbations will be incorporated into the model for refinement and increase of predictive values. In addition, humans will be screened in Project 3 for polymorphisms in key genes predicted to be involved in pathogenesis by our models, and cells from rare variants will be tested ex vivo for their response to influenza infection. By using an established well characterized human cohort for these studies we will investigate clinical outcomes associated with the variants. We hypothesize that our approach will result in the identification of novel host targets for therapeutic intervention during influenza virus infection.